I don't see a way to fix it but I made a mistake in the title. It's MISO that is pulled low. No way for the original poster to modify or delete a post??
To understand how we bring up the SPI block, you can read the source code for CyU3PSpiSetConfig() in [SDK Root]\firmware\lpp_source\cyu3spi.c.
But if I may ask, why do you need direct register writes to configure the block? The CyU3PSpiSetConfig function is already does what you want.
Thank you. That file should be able to help. The reason I'm doing this is that I want my PC application to read data from the flash over USB when the default bootloader is running. I want to use that data to determine which image to download into the FX3 for USB boot. I know I can download the flash reading image and read the flash but then I have to do a hard reset and the FX3 will start up into default bootloader again then I have to know that this is the device I just worked with and remember which image I want to download. It's a lot of extra steps. I don't see the default bootloader having any vendor requests to read the flash so I am just going to use the default bootloaders memory access request to configure the SPI and read a few hundred bytes from the flash. I'm 80% of the way there and it's not that hard so I think I'll continue on trying to get this working. Thanks again.